This software is designed to analyze biological sequence alignments and create median networks as well as Steiner trees. Its main application is in the field of bioinformatics, where it enables researchers to better understand the evolutionary relationships between different organisms.
Murka is a free software designed to help users infer parsimonistic phylogenies from alignments of biological sequences. This software is based on a combination of two algorithmic approaches, where building median networks, known for its usefulness in Phylogenetics, is combined with extracting Steiner trees from graphs. The result of this combination is the ability to offer almost complete coverage of the minimum cost trees from a source alignment while tolerating performance issues for many instances that are not easily solved by classical methods.
In addition to providing exact algorithms, Murka also offers heuristic methods to further assist users. It is important to note that while Murka is not the first program in this field, there are at least two publicly available and free software packages that target working with median networks. These software packages include Fluxus Engineering Network and AWC Spectronet. However, Murka distinguishes itself by being the first opensource program that is distributed under LGPL, and consequently, comes with no copyright limitations.
Murka includes a Steiner problem solver with a weak performance, but it can still solve the majority of medium-sized (2K-3K edges) SteinLib benchmarks in reasonable time. It is also important to note that the input and output file formats are compatible with those used by Fluxus Network, and the Steiner solver works with STP files. For visualization of the resulting networks, we chose the .dot format of GraphViz software.
Murka is a command-line software that has been tested under both Linux and Windows platforms. Currently, two hardware platforms are supported, including x86(is-32) and ia-64 (Itanium2). Overall, Murka is a great alternative for those looking for a free software solution for inferring parsimonistic phylogenies.
In addition to providing exact algorithms, Murka also offers heuristic methods to further assist users. It is important to note that while Murka is not the first program in this field, there are at least two publicly available and free software packages that target working with median networks. These software packages include Fluxus Engineering Network and AWC Spectronet. However, Murka distinguishes itself by being the first opensource program that is distributed under LGPL, and consequently, comes with no copyright limitations.
Murka includes a Steiner problem solver with a weak performance, but it can still solve the majority of medium-sized (2K-3K edges) SteinLib benchmarks in reasonable time. It is also important to note that the input and output file formats are compatible with those used by Fluxus Network, and the Steiner solver works with STP files. For visualization of the resulting networks, we chose the .dot format of GraphViz software.
Murka is a command-line software that has been tested under both Linux and Windows platforms. Currently, two hardware platforms are supported, including x86(is-32) and ia-64 (Itanium2). Overall, Murka is a great alternative for those looking for a free software solution for inferring parsimonistic phylogenies.
What's New
Version 1.1.10: N/A